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, 11:48, 30 July 2010
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| ==== What is QUAL? ==== | | ==== What is QUAL? ==== |
| + | QUAL stands for query quality. It is an indicator for how accurate each base in the query sequence (SEQ) is. If QUAL is specified, there is a quality value for each base in SEQ. |
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| + | Quality is calculated based on the probability that a base is wrong, p, using the following formula: |
| + | <math>quality = -10 \log_{10}p</math> |
| + | This quality is called the [http://en.wikipedia.org/wiki/Phred_quality_score Phred Quality Score]. |
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| + | Since a human readable format is desired for SAM, 33 is added to the calculated quality in order to make it a printable character ranging from ! - ~. |
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| + | So, for SAM, the QUAL field is: |
| + | <math>QUAL = (-10 \log_{10}p) + 33</math> |
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| ==== What are TAGs? ==== | | ==== What are TAGs? ==== |